Background:
Hearing loss may be classified according to type (conductive, sensorineural or mixed) and onset (prelingual and postlingual) and may vary in severity. Hearing loss has been reported with X-linked, autosomal dominant or autosomal recessive inheritance (note: mitochondrial alterations associated with hearing loss are not a component of this panel). Approximately 1/500 newborns are affected by prelingual hearing loss – of these cases, roughly 50% have a genetic cause and 70% of these are non-syndromic; of these, the majority of autosomal recessive. The most common genetic cause of non-syndromic hearing loss is the recessive condition DFNB1, associated with mutations in GJB2. Of prelingual hearing loss, roughly 15% are associated with a known genetic syndrome. This next-generation sequencing test is designed to detect mutations in the coding region of 223 genes associated with hearing loss or are associated with syndromes that have hearing loss as a phenotypic feature.
Reasons for Referral:
- Confirmation of a clinical diagnosis of hearing loss.
- Carrier testing for individuals with a positive family history for hearing loss (targeted testing is available if familial mutation is known).
Methodology:
Next generation sequencing (NGS) will analyze the exons or coding regions of the genes using Illumina NextSeq 500/550 technology and preparing samples using hybridization probes to enrich exonic regions. This assay does not assess regions of insufficient coverage, introns and promoter regions; pseudogenes; where the reference genome is inaccurate or contains gaps and insertions; and regions of high GC or polynucleotide repeats, but may contain variants that impact gene function.
MT-RNR1 gene is sequenced by Sanger sequencing only. PCR amplification and sizing of product is utilized to perform break point analysis of the D13S1830 deletion of GJB6/Connexin 30
Exon-level deletion/duplication analysis is performed by running the NGS data through the Genome Analysis Toolkit (GATK) Germline Copy Number Variation best practices pipeline from GATK, version 4.1.4.1. A Bayesian model was validated clinically in our lab. The model can detect copy changes at a resolution of three (3) or more probe targets (exons) for deletions and duplications in genes that do not have pseudogenes, and is not designed to detect low-level mosaicism or balanced alterations.
Comprehensive Hearing Loss (223 genes)
A2ML1, ABHD12, ABHD5, ACOX1, ACTB, ACTG1, ADCY1, AIFM1, ALMS1, ANKH, AP1B1, ARSB, ARSG, ASIC5, ATOH1, ATP11A, ATP1A3, ATP2B2, ATP6V1B1, BCS1L, BDP1, BSND, BTD, C10orf2, CABP2, CACNA1D, CATSPER2, CCDC50, CD164, CDC14A, CDH23, CDKN1C, CEACAM16, CEP250, CEP78, CHD7, CIB2, CISD2, CLDN14, CLDN9, CLIC5, CLPP, CLRN1, CLRN2, COCH, COL11A1, COL11A2, COL1A1, COL2A1, COL4A3, COL4A4, COL4A5, COL4A6, COL9A1, COL9A2, CRYM, DCDC2, DFNA5, DFNB31, DFNB59, DIABLO, DIAPH1, DIAPH3, DLX5, DMXL2, DNAJC3, DNMT1, DSPP, DTNA, EDN3, EDNRB, ELMOD3, EPS8, EPS8L2, ERAL1, ESPN, ESRRB, EYA1, EYA4, FAM65B, FDXR, FGF3, FGFR3, FITM2, FOXC1, FOXI1, GATA3, GIPC3, GJB2, GJB3, GJB6, GPR98, GPRASP2, GPSM2, GRAP, GREB1L, GRHL2, GRXCR1, GRXCR2, HARS, HARS2, HGF, HOMER2, HOXA2, HSD17B4, IFNLR1, ILDR1, KARS, KCNE1, KCNJ10, KCNQ1, KCNQ4, KITLG, LARS2, LHFPL5, LMX1A, LOXHD1, LRTOMT, MAFB, MAP1B, MARVELD2, MASP1, MCM2, MEPE, MET, MIR96, MITF, MPZL2, MRPS2, MSRB3, MTRNR1, MYH14, MYH9, MYO15A, MYO3A, MYO6, MYO7A, NARS2, NDP, NLRP3, NOG, OPA1, OSBPL2, OTOA, OTOF, OTOG, OTOGL, P2RX2, PAX3, PCDH15, PDE1C, PDZD7, PEX1, PEX26, PEX6, PITX2, PLS1, PLS3, PNPT1, POLR1C, POLR1D, POU3F4, POU4F3, PRKCB, PRPS1, PTPRQ, RAI1, RDX, REEP6, REST, ROR1, RPS6KA3, S1PR2, SALL1, SALL4, SEMA3E, SERPINB6, SIX1, SIX2, SIX5, SLC17A8, SLC19A2, SLC22A4, SLC26A4, SLC26A5, SLC29A3, SLC44A4, SLC52A2, SLC52A3, SLC9A1, SLITRK6, SMPX, SNAI2, SOX10, SPNS2, STRC, SYNE4, TBC1D24, TBX1, TCOF1, TECTA, TIMM8A, TJP2, TMC1, TMEM126A, TMEM132E, TMEM43, TMIE, TMPRSS3, TNC, TPRN, TRIOBP, TRMT10C, TRRAP, TSHZ1, TSPEAR, TUBB4B, USH1C, USH1G, USH2A,WBP2,WFS1, XYLT2,
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5 mL
- Child: 5 mL
- Infant: 2-3 mL
Saliva: 2 ORAgene™ Saliva Collection Kit(s) (OGR-500) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample.
Assisted Saliva: 4 ORAgene™ Saliva Collection Kit(s) (OGR-575) used according to manufacturer instructions. Please contact KDL Client Services for a Saliva Collection Kit for patients that cannot provide a blood sample
Skin Fibroblast: Punch Biopsy (Cell cultures will be prepared at KDL and used for testing), or 2 T-25 confluent flasks.
DNA: 5-10 µg at a minimum of 60-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)
Prenatal:
Direct Amniotic Fluid (10-20mL)
Direct CVS
Direct POC
Cultured Amniocytes (2 T-25 flasks)
Cultured CVS (2 T-25 flasks)
Cultured Fetal Tissue: Product of Conception (2 T-25 flasks)
Cord Blood (1-2mL)
Notice Regarding Molecular Genetic Testing on Prenatal Specimens:
Maternal cell rule-out testing will be performed on all prenatal specimens received. Please provide maternal blood (or saliva) in addition to the fetal specimen. Additional charges apply for the maternal cell rule-out test.
For routine testing of blood and saliva (or DNA extracted from them), KDL does NOT accept samples from patients within two (2) weeks of a packed cell/platelet transfusion or within four (4) weeks of a whole blood transfusion. For extraordinary circumstances, where testing must be performed outside of the above windows, please contact our lab.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information, including ethnicity, clinical history, and family history.
Test Performed (Days):
Weekly
Turn Around Time:
Eight Weeks
Shipment Sensitivity Requirements:
- Package and ship specimen to remain cold, but not frozen.
- Ship via overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping kits and instructions at (855) 535-1522.
References:
Additional Info: